multipleGroupDEgenes: DE genes analysis for multiple groups.

In Tong-Chen/ImageGP: For ImageGP cloud platform (https://www.bic.ac.cn/BIC)

DE genes analysis for multiple groups.

Description

DE genes analysis for multiple groups.

Usage

multipleGroupDEgenes(
  dds,
  comparePairFile = NULL,
  design = "conditions",
  padj = 0.05,
  log2FC = 1,
  dropCol = c("lfcSE", "stat"),
  output_prefix = "ehbio",
  normalized_counts = NULL,
  lfcShrink = FALSE,
  ...
)

Arguments

dds	DESeq function returned object.
comparePairFile	A file containing sample groups for comparing. Optional. If not given, the function will use colData information in dds and perform group compare for all possible combinations. groupA groupB groupA groupC groupC groupB
design	The group column name. Default "conditions".
padj	Multiple-test corrected p-value. Default 0.05.
log2FC	Log2 transformed fold change. Default 1.
dropCol	Columns to drop in final output. Default c("lfcSE", "stat"). Other options "ID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj". This has no specific usages except make the table clearer.
output_prefix	A string as prefix of output files.
normalized_counts	a data matrix of normalized counts or an object return by deseq2normalizedExpr. Default NULL.
...	Additional parameters given to ggsave.

Examples

multipleGroupDEgenes(dds)

Tong-Chen/ImageGP documentation built on April 14, 2025, 12:54 p.m.